Patti Sapone/The Star-LedgerSusan Goodin, associate director for clinical trials and therapeutics at the Cancer Institute of New Jersey, said doctors are facing difficult conversations with patients when critical medicines are in short supply.

The nation’s ongoing shortage of cancer medicines isn’t making oncologist James Salwitz’s work any easier.

Salwitz, who practices in New Brunswick, has been forced to tell some of his patients that the drug he would prefer to treat them with is unavailable. The alternative, he has to tell them, won’t be as effective and will cause more side effects.

"In the U.S., we’re having two conversations (with patients) that produce the same result,’’ Salwitz said, "One is that a drug is too expensive and you may not be able to afford it and the other is the drug is too expensive to make, so we can’t get it anymore.’’

During the past year, there have been troubling shortages of medicines, including older but still critical cancer drugs such as Doxil, Taxol and Methotrexate — an old chemotherapy drug now used primarily to treat children with leukemia.

The reasons for the shortages, which began nearly four years ago and have grown more severe, range from manufacturing problems that have shut down suppliers and shortages of raw materials to pure economics — in some cases, pharmaceutical companies are choosing to stop making medicines that are no longer profitable.

Experts like Uwe Reinhardt, a Princeton University professor of economics and public policy, said he believes the main cause for the long-term shortages is one of profitability.

"If something were really profitable, they would do it,’’ Reinhardt said. "It’s instinctive to a company.’’

The shortages have left physicians and hospital pharmacy directors scrambling to find rationed medicines, choosing less desirable treatments and putting another hurdle between gravely ill patients and their quality of life.

Susan Goodin, associate director for clinical trials and therapeutics at the Cancer Institute of New Jersey, said every time a new shortage is identified, she has to have another discussion with doctors about managing supplies and choosing alternative treatments.

"Physicians are facing this difficult heart-to-heart conversation with patients,’’ Goodin said, "about how we don’t have the drug to treat them.’’

Maureen Maurer, Morristown Medical Center’s pharmacy operations coordinator, said two months ago, she was spending between six and eight hours a day on the telephone with doctor’s offices, hospitals and distributors, scrounging for doses of methotrexate particularly. In some cases, hospitals will share or swap some of the scarce medicines with one another or with doctor’s offices or drug distributors, Maurer said.

The drug supplies go up and down. As the shortage of methotrexate eased — there is no alternative, making its scarcity more dire for patients — Maurer spent less time on the telephone trying to find doses of the drug.

"Now, I’m spending about an hour every other day on the phone,’’ she said. "We’re all helping each other.’’

Maurer said there have been few signs that Doxil is getting any easier to find. "I understand more is supposed to be becoming available,’’ she said, "but I’m not optimistic that there will be much.’’

Doxil, which is marketed by Johnson & Johnson’s Janssen Pharmaceuticals subsidiary, is one of the most vexing cancer drug shortages. The drug is used to treat a variety of cancers, including recurring ovarian cancer, breast cancer and sarcomas — or soft tissue cancers. Physicians often favor it over other drugs because it can be more effective, produce fewer side effects and help some patients survive three or four years longer with the disease.

"It’s changing the way patients are treated, all of these shortages are, but this one especially,’’ Salwitz said of Doxil. "You’re dealing with patients who are fighting for their lives and fighting to maintain a quality of life,’’ he said, "It’s really a terrible thing to do to people.’’

Janssen’s injectible drug has been manufactured for more than a decade by a single supplier, Ohio-based Ben Venue Laboratories, one of a few companies capable of carrying out the complex, multi-step manufacturing process required to make it. The company, owned by German drug maker Boehringer Ingelheim, stopped producing the drug late last year after spending several years trying to address manufacturing and quality control problems.

In December, Ben Venue said it had been working with global regulatory agencies over the past few years to balance the need to produce critical medicines while it addressed manufacturing and quality control -related issues at its plant.

"Ben Venue can no longer continue to manufacture and remediate simultaneously and must direct its focus on addressing manufacturing-related issues,’’ the company said in a statement.

Janssen responded to the problem by creating a special program that would help ensure that an estimated 3,300 patients being treated with Doxil would continue to receive it. And then, in an effort to ease the shortages, federal drug regulators allowed a rare, temporary importation of a similar drug called Lipodox from India.

Under a special provision, the Food and Drug Administration is allowing Caraco Pharmaceutical Laboratories, a generic drug maker, to import Lipodox from Sun Pharmaceutical, its parent company in Mumbai.

Earlier this month, with supplies of Doxil waning, Janssen asked physicians to supply them with information about the status of patients in the program and to provide a count of those who needed to be re-enrolled. No new patients are being accepted into the program.

Meanwhile, Johnson & Johnson said it is working to find a second company to work with Ben Venue to begin resupplying the medicine in the fall — a few months earlier than its original estimates, according to Lisa Vaga, a company spokeswoman.

Maurer, the pharmacy coordinator at Morristown Medical Center, said the hospital has "a handful’’ of patients being treated with Doxil and so far, it has managed to get the supply it needs. "If we were desperate, we would buy Lipodox,’’ she said.

It could come to that.

Maurer said the medical center is using Doxil to treat a HIV patient suffering with sarcoma. "It’s not something you would usually use, but it’s the one thing the patient has responded to and it’s keeping his disease in check,’’ she said.

So far, Maurer has succeeded in getting enough of the drug through her network of pharmacists. "If we say we need this much by this date, generally someone responds,’’ she said.

Salwitz worries about having to put some of his patients on different drugs.

When one of his ovarian cancer patients had a recurrence, he began treating her with another chemotherapy drug, Adriamycin or doxorubicin. "She was really sick. All of her hair fell out and then when Doxil was available, she wasn’t in any shape to be treated,’’ he said.

A professor at Robert Wood Johnson Medical School, Salwitz said the steady shortages of medicines are likely to continue unless new policies are put in place to regulate drug makers in other parts of the world and allow them to begin selling their medicines to the U.S.

"As long as we only make decisions based on a purely closed capitalistic system, we’re going to have these flaws,’’ he said. "It doesn’t matter whether people who need the medicines get them, the system is based on a drug maker’s ability to make a profit.’’

Goodin, who runs the pharmacy at the Cancer Institute of New Jersey, said she continues to monitor available supplies of Doxil and Lipodox. "We’re going through both programs and spending a significant amount of time trying to allocate the drug appropriately,’’ she said.

"I ask myself all the time, how can this be happening,’’ Goodin said. "It’s astounding.’’